It tells me to clear out App.xaml.cs. After looking at PhoneBootstrapper, it doesn't seem to have the "new" features that are in the WP8 app.xaml.cs templates. I take I have to custom-delete app.xaml.cs to match what's not in the the box?

The main reason for asking is - How would I detect that (at some later point in time) CM comes with this in the box?

To be honest there wasn't much done to CM to make it ready for use with WP8, it just worked. Most of the features were carried over minor tweaks to the source to make it not show duplications on build related to the 4.5 Framework changes that were
present.

If you want the features add them to the bootstrap to make your app easier to localize, it wouldn't be that hard to do that with the overrides that are available in the bootstrap